Only about 250,000 people attend P-Nats games each year, and how many of those are unique? Probably 100,000 or fewer (maybe a lot fewer). How many of those would NOT attend Nationals games or become Nationals fans? I actually think it would be a tougher decision if the minor league club was farther away. You might lose Harrisburg fans to Pittsburgh or Philly if you move that affiliate, but what are the chances a PWC fan will abandon the Nationals for another team? You are within commuting distance of the ballpark!
I think if you have serious issues with a minor league club, the geographical convenience/synergy probably takes a back seat.